Showing : RNASEQ • reset
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
updated 16 hours ago by 50k • written 17 hours ago by • 0
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2
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137
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
4 days ago • updated 1 day ago catv • 0
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1
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103
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Log-cpm values from limma
limma edgeR RNASeq
updated 4 days ago by 50k • written 5 days ago by • 0
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1
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78
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 5 days ago by 41k • written 5 days ago by • 0
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1
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117
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Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 13 days ago by ★ 4.0k • written 15 days ago by • 0
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2
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210
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
4 weeks ago kcarey • 0
2
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2
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243
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
5 weeks ago Sabiha ▴ 20
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2
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233
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
5 weeks ago kcarey • 0
1
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4
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289
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DESeq2 Replicates
DESeq2 RNASeq
6 weeks ago kcarey • 0
1
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3
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337
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 7 weeks ago by ★ 1.3k • written 7 weeks ago by ▴ 10
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4
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271
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
7 weeks ago mperalc • 0
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2
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259
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Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
3
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5
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597
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 7 weeks ago by 41k • written 8 weeks ago by ▴ 10
2
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1
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241
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Limma Question
DESeq2 BatchEffect limma RNASeq
updated 8 weeks ago by 41k • written 8 weeks ago by ▴ 10
3
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6
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499
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Average biological replicates in RNA-seq
Mfuzz RNASeq
9 weeks ago • updated 8 weeks ago boczniak767 ▴ 720
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199
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
9 weeks ago Abril • 0
2
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2
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373
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Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
10 weeks ago jackafiore • 0
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2
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1.1k
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How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 11 months ago by • 0
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4
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370
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Ballgown error in scan for c.tab files
ballgown RNASeq
11 weeks ago candacenewcome • 0
1
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3
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318
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
12 weeks ago • updated 11 weeks ago island • 0
1
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3
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549
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Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 12 weeks ago by • 0
0
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1
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218
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 3 months ago by ▴ 190 • written 3 months ago by • 0
2
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4
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541
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Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
4
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6
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551
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 10 weeks ago by 50k • written 3 months ago by • 0
3
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1
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261
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Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 3 months ago by 50k • written 3 months ago by • 0
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3
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448
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dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 3 months ago by • 0
0
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1
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254
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DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
3 months ago WS • 0
2
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3
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1.1k
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Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 4 months ago by ★ 1.3k • written 4 months ago by • 0
1
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2
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428
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How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
1
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2
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417
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RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
4 months ago drewhaydensteele • 0
7
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2
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752
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limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 4 months ago by 50k • written 4 months ago by • 0
0
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3
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437
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago • updated 4 months ago Karthik • 0
1
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1
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366
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Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 4 months ago by 41k • written 5 months ago by • 0
2
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3
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446
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DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
5 months ago • updated 4 months ago Karthik • 0
2
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2
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388
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DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
5 months ago Manthos • 0
2
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4
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585
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limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
5 months ago Tyler Sagendorf ▴ 10
0
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1
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423
views
DESeq2 model for two genome system
RNASeq DESeq2
updated 5 months ago by 41k • written 6 months ago by • 0
0
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2
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518
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TCGA counts to TPM from recount3 do not seem to right
recount3 TCGA RNASeq
updated 5 months ago by ★ 1.0k • written 6 months ago by ▴ 190
0
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9
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2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 5 months ago by • 0 • written 6.5 years ago by ▴ 60
1
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4
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603
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controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
5 months ago Wending • 0
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0
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339
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Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
5 months ago mch • 0
4
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2
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584
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DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 5 months ago by 50k • written 5 months ago by ▴ 10
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6
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804
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DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
6 months ago • updated 5 months ago erika.maldonado-rosado • 0
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0
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325
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is Dada2 biased toward a particular sequence ?
virology dada2 amplican Sequencing RNASeq
6 months ago Sara • 0
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2
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622
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Will DESeq2 be appropriate tool for analysis?
RNASeq DESeq2
6 months ago Karthik • 0
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0
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260
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
6 months ago Florian • 0
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0
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324
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Pysam pileup and Rsamtools pileup output discrepancy
Pysam pileup Rsamtools RNASeq
6 months ago Xinqi • 0
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0
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324
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Using DADA2 for finding viral sequence variants
VariantDetection dada2 RNASeq
6 months ago Sara • 0
1
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1
reply
398
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 6 months ago by 65k • written 6 months ago by • 0
1
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7
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808
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DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 4 months ago by 50k • written 6 months ago by • 0
50 results • Page 1 of 1
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Comment: Trying to use enrichGO by Guido Hooiveld ★ 3.9k
It is indeed better. Anyway, did you notice this part in the output from `str(ortologos_filtrados)`: `$Gene.ID : int 115709372 115716460 …
Comment: Trying to use enrichGO by fernanda.backsouza • 0
I'm new here, but its better now?
Comment: Trying to use enrichGO by Guido Hooiveld ★ 3.9k
That did NOT really improve things...... Likely I wasn't clear enough, but with R-code I meant both the command you typed, as well as the o…
Comment: Trying to use enrichGO by fernanda.backsouza • 0
Thank you for yout time guido, 1) When the pvalueCutoff = 1 nothing change. 2) output from > `str(ortologos_filtrados) data.frame':…
Answer: Cannabis OrgDb by Guido Hooiveld ★ 3.9k
> library(AnnotationHub) > hub <- AnnotationHub() snapshotDate(): 2023-10-23 > query(hub, c("cannabis","orgdb") ) …
Votes
Answer: Cannabis OrgDb
DESeq2: How to find out how well the model fits the data?
Comment: DESeq2 - dispersion estimation when there is none
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
Answer: OrgDb for maize
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